Gut dysbiosis and small intestinal bacterial overgrowth as independent forms of gut microbiota disorders in cirrhosis

Table 1 Descriptive statistics of patients with and without small intestinal bacterial overgrowth

	Patients with SIBO (n = 24)	Patients without SIBO (n = 23)	P value
Age, yr	50 (39-59)	51 (37-58)	0.949
Male/female	12/12	11/12	0.557
Body mass index, kg/m2	25.0 (22.9-27.8)	24.1 (22.3-26.1)	0.302
Red blood cells, 1012/L	3.7 (3.3-4.2)	4.0 (3.6-4.3)	0.322
White blood cells, 109/L	3.6 (2.6-4.9)	4.0 (3.2-5.6)	0.437
Platelets, 109/L	78 (49-108)	90 (59-115)	0.229
C-reactive protein, mg/L	11.4 (1.6-17.1)	2.1 (0.1-9.2)	0.025
Serum albumen, g/L	35 (31-40)	36 (31-41)	0.617
Serum total bilirubin, μmol/L	36 (27-54)	38 (23-64)	0.848
Prothrombin (Quick test), %	57 (50-68)	64 (53-70)	0.233
Ascites, n (%)	17 (70.8)	10 (43.4)	0.054
Esophageal varices, n (%)	19 (79.2)	19 (82.6)	0.528
Spleen length, cm	16.2 (14.0-20.0)	14.6 (13.3-16.2)	0.080
Portal vein diameter, mm	13.0 (12.0-13.7)	12.0 (11.0-13.5)	0.263
Overt hepatic encephalopathy, n (%)	9 (37.5)	8 (34.8)	0.544
Child-Pugh score	8 (6-10)	8 (6-9)	0.551
Drugs used by patients within 6 mo prior to study enrollment
Proton pump inhibitors, n (%)	9 (37.5)	8 (34.8)	0.544
Beta blockers, n (%)	5 (20.8)	3 (13.0)	0.375
L-ornithine-L-aspartate, n (%)	4 (16.7)	4 (17.4)	0.625
Diuretics, n (%)	13 (54.2)	8 (34.8)	0.149
Ursodeoxycholic acid, n (%)	4 (16.7)	5 (21.7)	0.471
Glucocorticoids, n (%)	2 (8.3)	6 (26.1)	0.109
Antiviral drugs, n (%)	7 (29.2)	4 (17.4)	0.273

SIBO: Small intestinal bacterial overgrowth.

Table 2 Abundance of bacteria at the phylum and class levels in gut microbiome of patients with and without small intestinal bacterial overgrowth

Taxon	Patients with SIBO (n = 24)	Patients without SIBO (n = 23)	P value
Phyla
Firmicutes	90.2 (77.7-94.3)	80.0 (67.5-87.2)	0.017
Bacteroidetes	5.3 (1.5-7.7)	6.8 (5.6-1.3)	0.013
Proteobacteria	1.3 (0.2-3.0)	1.7 (0.2-4.1)	0.790
Actinobacteria	0.5 (0.3-1.6)	0.8 (0.4-3.8)	0.343
Fusobacteria	0.01 (0.00-0.03)	0.00 (0.00-0.00)	0.011
Main classes of Firmicutes
Clostridia	77.9 (67.1-84.6)	70.9 (61.6-83.1)	0.151
Bacilli	2.4 (0.4-7.1)	1.1 (0.4-7.3)	0.573
Negativicutes	0.5 (0.2-0.8)	0.4 (0.2-1.4)	0.956

SIBO: Small intestinal bacterial overgrowth.

Table 3 Abundance of bacteria at the family level in gut microbiome of patients with and without small intestinal bacterial overgrowth

Family	Patients with SIBO (n = 24)	Patients without SIBO (n = 23)	P value
Families of Clostridia
Lachnospiraceae	41.00 (29.71-55.82)	31.30 (17.55-43.85)	0.047
Ruminococcaceae	26.15 (13.79-35.50)	21.41 (14.89-34.43)	0.856
Peptostreptococcaceae	0.50 (0.18-2.72)	0.17 (0.04-1.13)	0.066
Clostridiaceae	0.30 (0.01-1.12)	0.10 (0.01-0.47)	0.463
Eubacteriaceae	0.00 (0.00-0.00)	0.00 (0.00-0.01)	0.463
Families of Bacilli
Streptococcaceae	1.46 (0.29-6.03)	0.41 (0.10-3.42)	0.170
Lactobacillaceae	0.23 (0.03-0.56)	0.10 (0.01-0.38)	0.413
Staphylococcaceae	0.02 (0.01-0.03)	0.01 (0.01-0.02)	0.450
Enterococcaceae	0.01 (0.00-0.04)	0.01 (0.00-0.23)	0.873
Family of Negativicutes
Veillonellaceae	0.43 (0.07-0.73)	0.16 (0.05-1.15)	0.632
Families of Bacteroidetes
Bacteroidaceae	1.13 (0.35-3.19)	3.77 (1.05-4.96)	0.014
Prevotellaceae	0.56 (0.01-3.12)	0.27 (0.04-3.07)	0.941
Porphyromonadaceae	0.11 (0.02-0.29)	0.40 (0.23-0.66)	0.002
Rikenellaceae	0.07 (0.01-0.74)	0.45 (0.06-1.35)	0.047
Families of Proteobacteria
Enterobacteriaceae	0.72 (0.02-2.13)	1.51 (0.05-2.81)	0.632
Moraxellaceae	0.04 (0.02-0.05)	0.02 (0.01-0.04)	0.014
Pasteurellaceae	0.01 (0.00-0.15)	0.00 (0.00-0.01)	0.025
Sutterellaceae	0.01 (0.00-0.06)	0.02 (0.00-0.05)	0.400
Desulfovibrionaceae	0.00 (0.00-0.01)	0.01 (0.00-0.03)	0.042
Families of Actinobacteria
Bifidobacteriaceae	0.46 (0.14-1.50)	0.65 (0.12-3.22)	0.366
Coriobacteriaceae	0.09 (0.07-0.14)	0.08 (0.04-0.20)	0.790
Actinomycetaceae	0.02 (0.01-0.04)	0.01 (0.00-0.03)	0.039
Micrococcaceae	0.02 (0.01-0.06)	0.01 (0.00-0.01)	0.045

SIBO: Small intestinal bacterial overgrowth.

Table 4 Abundance of bacteria at the genus level in gut microbiome of patients with and without small intestinal bacterial overgrowth

Genus	Family	Patients with SIBO (n = 24)	Patients without SIBO (n = 23)	P value
Blautia	Lachnospiraceae	13.38 (6.78-20.52)	6.99 (3.22-13.47)	0.020
Faecalibacterium	Ruminococcaceae	8.64 (3.65-19.55)	7.82 (3.02-12.74)	0.516
Gemmiger	Ruminococcaceae	2.33 (0.95-4.69)	1.65 (0.03-2.86)	0.237
Ruminococcus	Ruminococcaceae	1.80 (0.01-3.51)	0.58 (0.12-1.83)	0.617
Roseburia	Lachnospiraceae	1.66 (0.51-4.20)	0.92 (0.13-3.42)	0.377
Streptococcus	Streptococcaceae	1.36 (0.22-5.78)	0.37 (0.08-3.42)	0.151
Dorea	Lachnospiraceae	1.18 (0.63-2.51)	0.69 (0.42-1.35)	0.099
Bacteroides	Bacteroidaceae	1.15 (0.34-3.04)	3.59 (1.08-5.05)	0.012
Fusicatenibacter	Lachnospiraceae	0.79 (0.27-1.06)	0.13 (0.04-0.31)	0.003
Prevotella	Prevotellaceae	0.43 (0.01-2.27)	0.12 (0.01-2.19)	0.856
Escherichia	Enterobacteriaceae	0.38 (0.01-1.64)	0.28 (0.01-1.31)	0.890
Bifidobacterium	Bifidobacteriaceae	0.32 (0.11-1.15)	0.47 (0.07-2.39)	0.413
Oscillibacter	Oscillospiraceae	0.07 (0.01-0.15)	0.21 (0.09-0.38)	0.025
Alistipes	Rikenellaceae	0.06 (0.01-0.52)	0.41 (0.06-1.25)	0.025
Anaerostipes	Lachnospiraceae	0.62 (0.06-0.50)	0.49 (0.08-0.67)	0.170
Parabacteroides	Porphyromonadaceae	0.03 (0.00-0.11)	0.16 (0.05-0.29)	0.009
Acinetobacter	Moraxellaceae	0.03 (0.02-0.05)	0.02 (0.01-0.03)	0.004
Akkermansia	Akkermansiaceae	0.01 (0.00-0.71)	0.01 (0.00-1.33)	0.983
Oribacterium	Lachnospiraceae	0.01 (0.00-0.02)	0.00 (0.00-0.00)	0.040
Barnesiella	Porphyromonadaceae	0.00 (0.00-0.03)	0.03 (0.00-0.06)	0.025
Intestinimonas	Oscillospiraceae	0.00 (0.00-0.02)	0.03 (0.01-0.06)	0.015
Haemophilus	Pasteurellaceae	0.00 (0.00-0.10)	0.00 (0.00-0.01)	0.031

Genera with an abundance of < 1% and not significantly different between patient groups are not presented. SIBO: Small intestinal bacterial overgrowth.